Hi Wei,

Could you explain in more detail the type of analysis that you are interested in doing? Including a few lines of the BED file (5-10) pasted into the reply would be helpful.

Thanks,

Jen Galaxy Tea

On 6/10/10 11:14 AM, Yanwei Tan wrote:

Deal all,

I was wondering if anyone know Galaxy can analyze the New 5' start site, 3' end site and long internal coding exons. Because I just try to run Scripture (http://www.broadinstitute.org/software/scripture/Graph%20building) and got the bed file. Can someone give me some hint?

Many thanks in advance! Wei _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

"Hello Wei,

Thank you for sending more information and sample data.

The general query path would be to:

1) bring in the UCSC Genes 3' UTR annotation as a dataset (knownGene -> BED -> 3' UTR Exons -> Galaxy)

2) analyze your data versus these target transcripts by overlap using tools in the group "Operate on Genomic Intervals"

You may find it helpful to group transcripts and overlapping samples into gene clusters using the UCSC table knownIsoforms.

Hopefully this helps to get you started, Thanks, Jen

Galaxy Team

On 6/22/10 10:07 AM, Yanwei Tan wrote:

Hi Jen,

Thanks a lot for your reply! So please see the following bed file.

track name=junctions description="TopHat junctions" chr19 3262083 3264847 JUNC00000001 2 - 3262083 3264847 255,0,0 2 61,37 0,2727 chr19 3266410 3267296 JUNC00000002 2 - 3266410 3267296 255,0,0 2 49,55 0,831 chr19 3267271 3268345 JUNC00000003 3 - 3267271 3268345 255,0,0 2 65,48 0,1026 chr19 3268383 3268720 JUNC00000004 2 - 3268383 3268720 255,0,0 2 33,61 0,276 chr19 3272970 3274417 JUNC00000005 5 - 3272970 3274417 255,0,0 2 65,62 0,1385 chr19 3274528 3276802 JUNC00000006 1 - 3274528 3276802 255,0,0 2 28,47 0,2227 chr19 3276860 3279592 JUNC00000007 4 - 3276860 3279592 255,0,0 2 59,60 0,2672 chr19 3279962 3281488 JUNC00000008 2 - 3279962 3281488 255,0,0 2 34,70 0,1456 chr19 3281520 3282759 JUNC00000009 2 - 3281520 3282759 255,0,0 2 68,59 0,1180 chr19 3284771 3285362 JUNC00000010 2 + 3284771 3285362 255,0,0 2 46,53 0,538 chr19 3284779 3285344 JUNC00000011 2 + 3284779 3285344 255,0,0 2 54,35 0,530 chr19 3285352 3286924 JUNC00000012 2 + 3285352 3286924 255,0,0 2 43,50 0,1522 chr19 3289043 3291029 JUNC00000013 5 + 3289043 3291029 255,0,0 2 44,53 0,1933

I have stimulated sample and control sample, I would like to know if there is 3 UTR, 5 start site variance in the stimulated sample. There is always some interesting info in the 3 UTR. If the length of 3UTR changes under specific biological condition, then it could explain some mechanism, for example some microRNA info.

And so far, I uploaded the bed file to Galaxy, and choose from cdsEnd to txEnd (should be transcript end, right?) which should be 3 UTR info. If this is right, I check by hand every 3UTR of every gene compared with public annotation like UCSC. But this is not a proper way and time-consuming. I do not have bioinfomatics experience, do not know if one can give me some advice how to do this properly.

Many thanks for your help!

Best, Wei

On 6/22/10 6:35 PM, Jennifer Jackson wrote:

...

Hi Wei,

Could you explain in more detail the type of analysis that you are interested in doing? Including a few lines of the BED file (5-10) pasted into the reply would be helpful.

Thanks,

Jen Galaxy Tea

On 6/10/10 11:14 AM, Yanwei Tan wrote:

...

Deal all,

I was wondering if anyone know Galaxy can analyze the New 5' start site, 3' end site and long internal coding exons. Because I just try to run Scripture (http://www.broadinstitute.org/software/scripture/Graph%20building) and got the bed file. Can someone give me some hint?

Many thanks in advance! Wei _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user